Mapping the common antigenic determinants in avidin and streptavidin

An epitope scan analysis of the whole sequence of avidin and core streptavidin using polyclonal antibodies to these two antigens reveal the presence of multiple common epitopes in both the proteins. These antigenic determinants consist mostly of either identical or similar residues. The antibody recognition sites in both antigens are shown to be localized to homologous regions.

Sequence Specific Interaction between Promoter DNA and Escherichia coli RNA Polymerase: Comparative Thermodynamic Analysis with One Immobilized Partner

Sequence specific interaction between DNA and protein molecules has been a subject of active investigation for decades now. Here, we have chosen single promoter containing bacteriophage Delta D-III T7 DNA and Escherichia coli RNA polymerase and followed their recognition at the air-water interface by using the surface plasmon resonance (SPR) technique, where the movement of one of the reacting species is restricted by way of arraying them on an immobilized support. For the Langmuir monolayer studies, we used a RNA polymerase with a histidine tag attached to one of its subunits, thus making it an xcellent substrate for Ni(II) ions, while the SPR Studies were done using biotin-labeled DNA immobilized on a streptavidin-coated chip. Detailed analysis of the thermodynamic parameters as a function of concentration and temperature revealed that the interaction of RNA polymerase with T7 DNA is largely entropy driven (83 (+/- 12) kcal mol(-1)) with a positive enthalpy of 13.6 (+/- 3.6) kcal mol(-1), The free energy of reaction determined by SPR and Langmuir-Blodgett technique was -11 (+/- 2) and -15.6 kcal mol(-1), respectively. The ability of these methods to retain the specificity of the recognition process was also established.

Electrochemical Functionalization of a Gold Electrode with Redox-Active Self-Assembled Monolayer for Electroanalytical Application

The electrochemical functionalization of a Au electrode with a redox-active monolayer and the electroanalytical applications of the functionalized electrode are described. Reaction of the electrochemically derived o-quinone on the self-assembled monolayer (SAM) of 6-mercaptopurine (MPU) on a Au electrode gives a redox-active 4-(6-mercapto-purin-9-yl)benzene-1,2-diol (MPBD) self-assembly under optimized conditions. Electrochemical quartz crystal microbalance technique has been employed to follow the functionalization of the electrode in real time. Electrochemically derived o-quinone reacts at the N(9) position of the self-assembled MPU in neutral pH. Raman spectral measurement confirms the reaction of o-quinone on MPU self-assembly. MPBD shows a well-defined reversible redox response, characteristic of a surface-confined redox mediator at 0.21 V in neutral pH. The anodic peak potential (Epa) of MPBD shifts by −60 mV while changing the solution pH by 1 unit, indicating that the redox reaction involves two electrons and two protons. The surface coverage (Γ) of MPBD was 7.2 ± 0.3 × 10-12 mol/cm2. The apparent heterogeneous rate constant (ksapp) for MPBD was 268 ± 6 s-1. MPBD efficiently mediates the oxidation of nicotinamide adenine dinucleotide (NADH) and ascorbate (AA). A large decrease in the overpotential and significant increase in the peak current with respect to the unmodified electrode has been observed. Surface-confined MPBD has been successfully used for the amperometric sensing of NADH and AA in neutral pH at the nanomolar level.

Probing top-gated field effect transistor of reduced graphene oxide monolayer made by dielectrophoresis

We demonstrate a top-gated field effect transistor made of a reduced graphene oxide (RGO) monolayer (graphene) by dielectrophoresis. The Raman spectrum of RGO flakes of typical size of 5 mu m x 5 mu m shows a single 2D band at 2687 cm(-1), characteristic of single-layer graphene.The two-probe current-voltage measurements of RGO flakes, deposited in between the patterned electrodes with a gap of 2.5 mu m using ac dielectrophoresis, show ohmic behavior with a resistance of similar to 37 k Omega. The temperature dependence of the resistance (R) of RGO measured between 305 K and 393 K yields a temperature coefficient of resistance [dR/dT]/R similar to -9.5 x 10(-4)/K, the same as that of mechanically exfoliated single-layer graphene. The field-effect transistor action was obtained by electrochemical top-gating using a solid polymer electrolyte (PEO + LiClO4) and Pt wire. The ambipolar nature of graphene flakes is observed up to a doping level of similar to 6 x 10(12)/cm(2) and carrier mobility of similar to 50 cm(2)/V s. The source-drain current characteristics show a tendency of current saturation at high source-drain voltage which is analyzed quantitatively by a diffusive transport model. (C) 2010 Elsevier Ltd. All rights reserved.

Investigation of the effect of nonlocal scale on ultrasonic wave dispersion characteristics of a monolayer graphene

In this article, an ultrasonic wave propagation in graphene sheet is studied using nonlocal elasticity theory incorporating small scale effects. The graphene sheet is modeled as an isotropic plate of one-atom thick. For this model, the nonlocal governing differential equations of motion are derived from the minimization of the total potential energy of the entire system. An ultrasonic type of wave propagation model is also derived for the graphene sheet. The nonlocal scale parameter introduces certain band gap region in in-plane and flexural wave modes where no wave propagation occurs. This is manifested in the wavenumber plots as the region where the wavenumber tends to infinite or wave speed tends to zero. The frequency at which this phenomenon occurs is called the escape frequency. The explicit expressions for cutoff frequencies and escape frequencies are derived. The escape frequencies are mainly introduced because of the nonlocal elasticity. Obviously these frequencies are function of nonlocal scaling parameter. It has also been obtained that these frequencies are independent of y-directional wavenumber. It means that for any type of nanostructure, the escape frequencies are purely a function of nonlocal scaling parameter only. It is also independent of the geometry of the structure. It has been found that the cutoff frequencies are function of nonlocal scaling parameter (e(0)a) and the y-directional wavenumber (k(y)). For a given nanostructure, nonlocal small scale coefficient can be obtained by matching the results from molecular dynamics (MD) simulations and the nonlocal elasticity calculations. At that value of the nonlocal scale coefficient, the waves will propagate in the nanostructure at that cut-off frequency. In the present paper, different values of e(o)a are used. One can get the exact e(0)a for a given graphene sheet by matching the MD simulation results of graphene with the results presented in this paper. (C) 2010 Elsevier B.V. All rights reserved.

Strong nonlocalization induced by small scale parameter on terahertz flexural wave dispersion characteristics of a monolayer graphene

This paper presents the strong nonlocal scale effect on the flexural wave propagation in a monolayer graphene sheet. The graphene is modeled as an isotropic plate of one atom thick. Nonlocal governing equation of motion is derived and wave propagation analysis is performed using spectral analysis. The present analysis shows that the flexural wave dispersion in graphene obtained by local and nonlocal elasticity theories is quite different. The nonlocal elasticity calculation shows that the wavenumber escapes to infinite at certain frequency and the corresponding wave velocity tends to zero at that frequency indicating localization and stationary behavior. This behavior is captured in the spectrum and dispersion curves. The cut-off frequency of flexural wave not only depend on the axial wavenumber but also on the nonlocal scaling parameter. The effect of axial wavenumber on the wave behavior in graphene is also discussed in the present manuscript. (C) 2010 Elsevier B.V. All rights reserved.

Vesicle and Stable Monolayer Formation from Simple ``Click'' Chemistry Adducts in Water

Click chemistry has been successfully extended into the field of molecular design of novel amphiphatic adducts. After their syntheses and characterizations, we have studied their aggregation properties in aqueous medium. Each of these adducts forms stable suspensions in water. These suspensions have been characterized by dynamic light scattering (DLS) studies and transmission electron microscopy (TEM). The presence of inner aqueous compartments in such aggregates has been demonstrated using dye (methylene blue) entrapment studies. These aggregates have been further characterized using X-ray diffraction (XRD), which indicates the existence of bilayer structures in them. Therefore, the resulting aggregates could be described as vesicles. The temperature-induced order-to-disorder transitions of the vesicular aggregates and the accompanying changes in their packing and hydration have been examined using high-sensitivity differential scanning calorimetry, fluorescence anisotropy, and generalized polarization measurements using appropriate membrane-soluble probe, 1,6-diphenylhexatriene, and Paldan, respectively. The findings of these studies are consistent with each other in terms of the apparent phase transition temperatures. Langmuir monolayer studies confirmed that these click adducts also form stable monolayers on buffered aqueous subphase at the air-water interface.

Composition Driven Monolayer to Bilayer Transformation in a Surfactant Intercalated Mg-Al Layered Double Hydroxide

The structure and organization of dodecyl sulfate (DDS) surfactant chains intercalated in an Mg-Al layered double hydroxide (LDH), Mg(1-x)Alx(OH)(2), with differing Al/Mg ratios has been investigated. The Mg-Al LDHs can be prepared over a range of compositions with x varying from 0.167 to 0.37 and therefore provides a simple system to study how the organization of the alkyl chains of the intercalated DDS anions change with packing density; the Al/Mg ratio or x providing a convenient handle to do so. Powder X-ray diffraction measurements showed that at high packing densities (x >= 0.3) the alkyl chains of the intercalated dodecyl sulfate ions are anchored on opposing LDH sheets and arranged as bilayers with an interlayer spacing of similar to 27 angstrom. At lower packing densities (x < 0.2) the surfactant chains form a monolayer with the alkyl chains oriented flat in the galleries with an interlayer spacing of similar to 8 angstrom. For the in between compositions, 0.2 <= x < 0.3, the material is biphasic. MD simulations were performed to understand how the anchoring density of the intercalated surfactant chains in the Mg-Al LDH-DDS affects the organization of the chains and the interlayer spacing. The simulations are able to reproduce the composition driven monolayer to bilayer transformation in the arrangement of the intercalated surfactant chains and in addition provide insights into the factors that decide the arrangement of the surfactant chains in the two situations. In the bilayer arrangement, it is the dispersive van der Waals interactions between chains in opposing layers of the anchored bilayer that is responsible for the cohesive energy of the solid whereas at lower packing densities, where a monolayer arrangement is favored, Coulomb interactions between the positively charged Mg-Al LDH sheets and the negatively charged headgroup of the DDS anion dominate.

Ultrasonic wave characteristics of a monolayer graphene on silicon substrate

The present work deals with an ultrasonic type of wave propagation characteristics of monolayer graphene on silicon (Si) substrate. An atomistic model of a hybrid lattice involving a hexagonal lattice of graphene and surface atoms of diamond lattice of Si is developed to identify the carbon-silicon bond stiffness. Properties of this hybrid lattice model is then mapped into a nonlocal continuum framework. Equivalent force constant due to Si substrate is obtained by minimizing the total potential energy of the system. For this equilibrium configuration, the nonlocal governing equations are derived to analyze the ultrasonic wave dispersion based on spectral analysis. From the present analysis we show that the silicon substrate affects only the flexural wave mode. The frequency band gap of flexural mode is also significantly affected by this substrate. The results also show that, the silicon substrate adds cushioning effect to the graphene and it makes the graphene more stable. The analysis also show that the frequency bang gap relations of in-plane (longitudinal and lateral) and out-of-plane (flexural) wave modes depends not only on the y-direction wavenumber but also on nonlocal scaling parameter. In the nonlocal analysis, at higher values of the y-directional wavenumber, a decrease in the frequency band gap is observed for all the three fundamental wave modes in the graphene-silicon system. The atoms movement in the graphene due to the wave propagation are also captured for all the tree fundamental wave modes. The results presented in this work are qualitatively different from those obtained based on the local analysis and thus, are important for the development of graphene based nanodevices such as strain sensor, mass and pressure sensors, atomic dust detectors and enhancer of surface image resolution that make use of the ultrasonic wave dispersion properties of graphene. (C) 2011 Elsevier Ltd. All rights reserved.

Crystallization of SrCO3 on a self-assembled monolayer substrate: an in-situ synchrotron X-ray study

Self-assembled monolayers (SAMs) of alkanethiols on gold surfaces show great promise in controlling the nucleation and growth of inorganic minerals from solution. In doing so, they mimic the role of some biogenic macromolecules in natural biomineralisation processes. Crystallization on SAM surfaces is usually monitored ex-situ; by allowing the process to commence and to evolve for some time, removing the substrate from the mother solution, and then examining it using microscopy, diffraction etc. We present here for the first time, the use of high energy monochromatic synchrotron X-radiation in conjunction with a two dimensional detector to monitor in situ, in a time resolved fashion, the growth of SrCO3 (strontianite) crystals on a SAM substrate.

Shear banding in a yield stress bearing Langmuir monolayer

We examine the shear-thinning behaviour of a two dimensional yield stress bearing monolayer of sorbitan tristearate at air/water interface. The flow curve consists of a linear region at low shear stresses/shear rates, followed by a stress plateau at higher values. The velocity profile obtained from particle imaging velocimetry indicates that shear banding occurs, showing coexistence of the fluidized region near the rotor and solid region with vanishing shear-rate away from the rotor. In the fluidized region, the velocity profile, which is linear at low shear rates, becomes exponential at the onset of shear-thinning, followed by a time varying velocity profile in the plateau region. At low values of constant applied shear rates, the viscosity of the film increases with time, thus showing aging behaviour like in soft glassy three-dimensional (3D) systems. Further, at the low values of the applied stress in the yield stress regime, the shear-rate fluctuations in time show both positive and negative values, similar to that observed in sheared 3D jammed systems. By carrying out a statistical analysis of these shear-rate fluctuations, we estimate the effective temperature of the soft glassy monolayer using the Galavatti-Cohen steady state fluctuation relation.

Symmetry-dependent phonon renormalization in monolayer MoS2 transistor

A strong electron-phonon interaction which limits the electronic mobility of semiconductors can also have significant effects on phonon frequencies. The latter is the key to the use of Raman spectroscopy for nondestructive characterization of doping in graphene-based devices. Using in situ Raman scattering from a single-layer MoS2 electrochemically top-gated field-effect transistor (FET), we show softening and broadening of the A(1g) phonon with electron doping, whereas the other Raman-active E-2g(1) mode remains essentially inert. Confirming these results with first-principles density functional theory based calculations, we use group theoretical arguments to explain why the A(1g) mode specifically exhibits a strong sensitivity to electron doping. Our work opens up the use of Raman spectroscopy in probing the level of doping in single-layer MoS2-based FETs, which have a high on-off ratio and are of technological significance.

Nonlocal continuum mechanics based ultrasonic flexural wave dispersion characteristics of a monolayer graphene embedded in polymer matrix

Wave propagation in graphene sheet embedded in elastic medium (polymer matrix) has been a topic of great interest in nanomechanics of graphene sheets, where the equivalent continuum models are widely used. In this manuscript, we examined this issue by incorporating the nonlocal theory into the classical plate model. The influence of the nonlocal scale effects has been investigated in detail. The results are qualitatively different from those obtained based on the local/classical plate theory and thus, are important for the development of monolayer graphene-based nanodevices. In the present work, the graphene sheet is modeled as an isotropic plate of one-atom thick. The chemical bonds are assumed to be formed between the graphene sheet and the elastic medium. The polymer matrix is described by a Pasternak foundation model, which accounts for both normal pressure and the transverse shear deformation of the surrounding elastic medium. When the shear effects are neglected, the model reduces to Winkler foundation model. The normal pressure or Winkler elastic foundation parameter is approximated as a series of closely spaced, mutually independent, vertical linear elastic springs where the foundation modulus is assumed equivalent to stiffness of the springs. For this model, the nonlocal governing differential equations of motion are derived from the minimization of the total potential energy of the entire system. An ultrasonic type of flexural wave propagation model is also derived and the results of the wave dispersion analysis are shown for both local and nonlocal elasticity calculations. From this analysis we show that the elastic matrix highly affects the flexural wave mode and it rapidly increases the frequency band gap of flexural mode. The flexural wavenumbers obtained from nonlocal elasticity calculations are higher than the local elasticity calculations. The corresponding wave group speeds are smaller in nonlocal calculation as compared to local elasticity calculation. The effect of y-directional wavenumber (eta(q)) on the spectrum and dispersion relations of the graphene embedded in polymer matrix is also observed. We also show that the cut-off frequencies of flexural wave mode depends not only on the y-direction wavenumber but also on nonlocal scaling parameter (e(0)a). The effect of eta(q) and e(0)a on the cut-off frequency variation is also captured for the cases of with and without elastic matrix effect. For a given nanostructure, nonlocal small scale coefficient can be obtained by matching the results from molecular dynamics (MD) simulations and the nonlocal elasticity calculations. At that value of the nonlocal scale coefficient, the waves will propagate in the nanostructure at that cut-off frequency. In the present paper, different values of e(0)a are used. One can get the exact e(0)a for a given graphene sheet by matching the MD simulation results of graphene with the results presented in this article. (c) 2012 Elsevier Ltd. All rights reserved.

SCALE EFFECTS ON ULTRASONIC WAVE DISPERSION CHARACTERISTICS OF MONOLAYER GRAPHENE EMBEDDED IN AN ELASTIC MEDIUM

Ultrasonic wave propagation in a graphene sheet, which is embedded in an elastic medium, is studied using nonlocal elasticity theory incorporating small-scale effects. The graphene sheet is modeled as an one-atom thick isotropic plate and the elastic medium/substrate is modeled as distributed springs. For this model, the nonlocal governing differential equations of motion are derived from the minimization of the total potential energy of the entire system. After that, an ultrasonic type of wave propagation model is also derived. The explicit expressions for the cut-off frequencies are also obtained as functions of the nonlocal scaling parameter and the y-directional wavenumber. Local elasticity shows that the wave will propagate even at higher frequencies. But nonlocal elasticity predicts that the waves can propagate only up to certain frequencies (called escape frequencies), after which the wave velocity becomes zero. The results also show that the escape frequencies are purely a function of the nonlocal scaling parameter. The effect of the elastic medium is captured in the wave dispersion analysis and this analysis is explained with respect to both local and nonlocal elasticity. The simulations show that the elastic medium affects only the flexural wave mode in the graphene sheet. The presence of the elastic matrix increases the band gap of the flexural mode. The present results can provide useful guidance for the design of next-generation nanodevices in which graphene-based composites act as a major element.

Thermal vibration analysis of monolayer graphene embedded in elastic medium based on nonlocal continuum mechanics

This paper presents the thermal vibration analysis of single-layer graphene sheet embedded in polymer elastic medium, using the plate theory and nonlocal continuum mechanics for small scale effects. The graphene is modeled based on continuum plate theory and axial stress caused by the thermal effects is also considered. Nonlocal governing equation of motion for this graphene sheet system is derived from the principle of virtual displacements. The closed form solution for thermal-vibration frequencies of a simply supported rectangular nanoplate has been obtained by using the Navier's method of solution. Numerical results obtained by the present theory are compared with available solutions in the literature and the molecular dynamics results. The influences of the small scale coefficient, the room or low temperature, the high temperature, the half wave number and the aspect ratio of nanoplate on the natural frequencies are considered and discussed in detail. The thermal vibration analysis of single- and double-layer graphene sheets are considered for the analysis. The mode shapes of the respective graphene system are also captured in this work. The present analysis results can be used for the design of the next generation of nanodevices that make use of the thermal vibration properties of the graphene.